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Mathematical Properties of the Deep Coalescence Cost

Content Provider	ACM Digital Library
Author	Rosenberg, Noah A. Than, Cuong V.
Abstract	In the minimizing-deep-coalescences (MDC) approach for species tree inference, a tree that has the minimal deep coalescence cost for reconciling a collection of gene trees is taken as an estimate of the species tree topology. The MDC method possesses the desirable Pareto property, and in practice it is quite accurate and computationally efficient. Here, in order to better understand the MDC method, we investigate some properties of the deep coalescence cost. We prove that the unit neighborhood of either a rooted species tree or a rooted gene tree under the deep coalescence cost is exactly the same as the tree's unit neighborhood under the rooted nearest-neighbor interchange (NNI) distance. Next, for a fixed species tree, we obtain the maximum deep coalescence cost across all gene trees as well as the number of gene trees that achieve the maximum cost. We also study corresponding problems for a fixed gene tree.
Starting Page	61
Ending Page	72
Page Count	12
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2012.133
Volume Number	10
Issue Number	1
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2013-01-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Vegetation,Topology,Computational biology,Bioinformatics,Upper bound,Sorting,Transforms,nearest-neighbor interchange,Deep coalescence,gene tree reconcilation,incomplete lineage sorting,maximal subtrees
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

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